The broad, overall objective of this work is to develop novel anti-infective agents which target the isoprene biosynthesis pathways in protozoa and bacteria by using a combination of x-ray crystallography, NMR spectroscopy, calorimetry, enzyme and cell growth inhibition assays, QSAR (quantitative structure-activity relationship) techniques, quantum chemistry, synthesis, drug delivery and animal testing. The First Specific Aim is to use x-ray crystallography and solid-state NMR spectroscopy to investigate the structures of novel inhibitors bound to, primarily, farnesyl diphosphate synthase (FPPS) from Trypanosoma cruzi (the causative agent of American trypanosomiasis or Chagas disease), Trypanosoma brucei (the causative agent of African sleeping sickness), E. coli and Staphylococcus aureus, as well as human FPPS (the target for the bisphosphonate drugs used in treating bone resorption diseases, of interest in the context of designing inhibitor selectivity). Solid-state NMR will be used to complement the crystallographic results by providing dynamics (from 2H NMR) and protonation state information (from 13C, 15N, 31P chemical shifts) for use in the QSAR investigations. The Second Specific Aim is to investigate structure-function relationships. We will investigate inhibitor binding by using isothermal titration calorimetry and differential scanning calorimetry, as well as by using classical enzyme inhibition techniques, to deduce ligand binding constants (KB) and Kis together with thermodynamics of binding information for the systems studied in Aim 1. In addition, inhibitor binding to human bone and bone mineral models will be investigated using chromatographic and NMR techniques. These results will all then be analyzed by using QSAR methods, including the use of differential QSAR methods (to optimize parasite/bacterial inhibition versus human FPPS inhibition, and to minimize bone adsorption), together with the use of non-conventional QM descriptors and 2H NMR order parameters, to enhance the predictive utility of these methods. The Third and Final Specific Aim is to use the results from Aims 1 and 2 to design and then synthesize specific inhibitors of the isoprene biosynthesis pathway. These inhibitors will include novel pyridium, sulfonium and phosphonium species and will be designed to target unique polar residues found in the active site of the protozoal and bacterial enzymes. These inhibitors will then be formulated in bioavailable forms for use in animal testing. We will also focus on synergistic or combination therapy approaches by using two or three compounds, each of which target the isoprene biosynthesis pathway: such strongly synergistic interactions have already been observed and now need to be optimized using the novel inhibitors. Lay Summary: The research proposed is designed to lead to new therapeutic approaches to treat a variety of infectious diseases. In the US, these diseases are primarily bacterial and are a major public health threat while in the rest of the world, infectious diseases are mainly caused by protozoa. This work seeks to develop drugs to treat both sorts of disease.